Variant report

Variant	rs12060391
Chromosome Location	chr1:98019997-98019998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12066229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116925	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17368985	1.00[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2786522	1.00[ASN][1000 genomes]
rs2786529	1.00[ASN][1000 genomes]
rs2786533	1.00[ASN][1000 genomes]
rs2811218	1.00[ASN][1000 genomes]
rs2811219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2811220	1.00[ASN][1000 genomes]
rs2811221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7530858	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540983	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv830703	chr1:97907708-98101144	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv933197	chr1:98003867-98039582	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv871708	chr1:98003908-98056575	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv546866	chr1:98003908-98078993	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97976600-98054200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:97976800-98051400	Weak transcription	Left Ventricle	heart
3	chr1:97988200-98023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:97996000-98037400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:97998600-98063800	Weak transcription	Right Ventricle	heart
6	chr1:97999400-98064600	Weak transcription	Psoas Muscle	Psoas
7	chr1:97999400-98074000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:98001200-98062400	Weak transcription	Fetal Lung	lung
9	chr1:98002000-98054600	Weak transcription	Lung	lung
10	chr1:98002000-98069400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:98002800-98058800	Weak transcription	Gastric	stomach
12	chr1:98003800-98022800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:98004400-98022200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:98004400-98058400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:98004800-98022800	Weak transcription	Fetal Intestine Small	intestine
16	chr1:98006400-98040600	Weak transcription	Pancreas	Pancrea
17	chr1:98007800-98058400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:98007800-98075800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:98008000-98021200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:98009800-98076800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:98009800-98112200	Weak transcription	HSMM	muscle
22	chr1:98010000-98021000	Weak transcription	Primary B cells from cord blood	blood
23	chr1:98012000-98054200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:98012200-98026400	Weak transcription	Aorta	Aorta
25	chr1:98012600-98036400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:98013000-98021600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:98013400-98048600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:98013600-98021800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:98013600-98022800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:98013600-98036400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:98013600-98058800	Weak transcription	Esophagus	oesophagus
32	chr1:98014000-98024400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:98015200-98021000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:98015200-98023000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:98015200-98038000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:98015200-98040200	Weak transcription	HSMMtube	muscle
37	chr1:98015200-98047000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:98015200-98054000	Weak transcription	Adipose Nuclei	Adipose
39	chr1:98015200-98058600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:98015200-98062000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:98015400-98038800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:98015600-98020200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:98015600-98023200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:98015600-98034600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:98015600-98058600	Weak transcription	Osteobl	bone
46	chr1:98016200-98023000	Weak transcription	Dnd41	blood
47	chr1:98016400-98023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:98017000-98036400	Weak transcription	NHDF-Ad	bronchial
49	chr1:98018400-98024200	Strong transcription	Liver	Liver
50	chr1:98018400-98040400	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links